In interviews promoting The Bourne Ultimatum, Matt Damon has argued that his Jason Bourne has supplanted James Bond as the hero of our time. “Bond is an imperialist and a misogynist,” Damon said, sounding not a little like his mentor, lefty historian Howard Zinn. “Bourne’s not the government. The government is after him. . . . He’s the opposite of James Bond.”

Maybe Damon was thinking of the Roger Moore 007 of The Spy Who Loved Me, because Daniel Craig’s Bond in last year’s Casino Royale doesn’t really fit his description. That Bond not only proves (relatively) monogamous and romantic but also is prey to doubts about the validity and the good intentions of the imperialist outfit he works for.

Neither has Bond been the only traditional hero with second thoughts about those he or she has pledged to serve. In Live Free or Die Hard, Bruce Willis’s maverick cop John McClane, never one to suffer police red tape or bureaucratic stuffed shirts in silence, takes on the incompetence and the treachery of the Department of Homeland Security as he battles with little more than his bare hands a superhacker terrorist who turns the government’s network of surveillance and control against itself.

Action heroes aren’t the only ones confronting the institutions and ideals they always believed in. In Harry Potter and the Order of the Phoenix, the boy wizard contends not just with puberty but also with the realization that the he and hierarchy at the Ministry of Magic might not be on the same page. They won’t join him in the fight against Voldemort; in fact, they cover up evidence of the evil lord’s existence. When their minion Dolores Umbridge, the ultimate apparatchik (imagine Alberto Gonzales in a pink dress), usurps Dumbledore as head of Hogwarts, Harry and his student pals defy the repressive regime’s edicts and form a subversive, secret army of their own.

Maybe the fundamentalist groups demanding a ban on J.K. Rowling’s novels are onto something. Harry might not be seducing kids into the black arts, but he sure is suggesting that they challenge authority. Those same religious groups are going to be even more pissed off at Chris Weitz’s upcoming adaptation of The Golden Compass, the first volume in Philip Pullman’s His Dark Materials trilogy. (It’s due for release on December 7.) As in the Harry Potter series, the protagonist, a girl this time (I always thought Hermione had more on the ball than Harry), is shocked by the realization that the socially accepted notions of order, of good and evil, even of time and space, are all a deception. Compelled to act, she’s drawn into a conflict with a wicked power structure that extends beyond the tyranny of her own situation to include all of society and organized religion and God Himself. Like the young girl in Guillermo del Toro’s brilliant El laberinto del fauno|Pan’s Labyrinth, who delves into fairy-tale fantasy to overcome her sadistic, Fascist stepfather, Pullman’s heroine must draw on her imagination, intuition, and integrity to defeat a malignant patriarchy.

So Damon’s Bourne is neither the first nor the last when it comes to movie heroes who were agents of a system they’re now seeking to overthrow it or purge of corruption. He may, however, be one of the first to come to terms with his own responsibility for the prevailing evil. “Why did you choose me?” he demands of those who shaped him. But the first step in regaining his identity and restoring justice is to acknowledge that the choice, from the beginning, was his own.